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Yorodumi- PDB-3ap5: Crystal structure of the galectin-8 N-terminal carbohydrate recog... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ap5 | ||||||
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Title | Crystal structure of the galectin-8 N-terminal carbohydrate recognition domain | ||||||
Components | Galectin-8 | ||||||
Keywords | SUGAR BINDING PROTEIN / Beta-Sandwich / Galectin / Carbohydrate/Sugar Binding | ||||||
Function / homology | Function and homology information lymphatic endothelial cell migration / xenophagy / cellular response to virus / integrin binding / cytoplasmic vesicle / carbohydrate binding / extracellular space / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å | ||||||
Authors | Matsuzaka, T. / Ideo, H. / Yamashita, K. / Nonaka, T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Galectin-8-N-domain recognition mechanism for sialylated and sulfated glycans Authors: Ideo, H. / Matsuzaka, T. / Nonaka, T. / Seko, A. / Yamashita, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ap5.cif.gz | 45.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ap5.ent.gz | 31.6 KB | Display | PDB format |
PDBx/mmJSON format | 3ap5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ap5_validation.pdf.gz | 419.8 KB | Display | wwPDB validaton report |
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Full document | 3ap5_full_validation.pdf.gz | 419.8 KB | Display | |
Data in XML | 3ap5_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 3ap5_validation.cif.gz | 11.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/3ap5 ftp://data.pdbj.org/pub/pdb/validation_reports/ap/3ap5 | HTTPS FTP |
-Related structure data
Related structure data | 3ap4C 3ap6C 3ap7C 3ap9C 3apbS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17423.123 Da / Num. of mol.: 1 / Fragment: N-terminal carbohydrate recognition domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS8 / Plasmid: pGEX-6P-2 / Production host: Escherichia coli (E. coli) / References: UniProt: O00214 |
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#2: Water | ChemComp-HOH / |
Sequence details | THIS RESIDUE IS CAUSED BY NATURAL VARIANT. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.44 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.275mM protein, 10mM Hepes-NaOH, 50mM sodium chloride, 0.5mM DTT, 125mM ammonium fluoride, 8% PEG 3350 , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1.28 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 26, 2005 |
Radiation | Monochromator: double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→34.021 Å / Num. all: 15467 / Num. obs: 15467 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.5 % / Biso Wilson estimate: 25.591 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 |
Reflection shell | Resolution: 1.92→1.97 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 7.5 / Num. unique all: 1112 / Rsym value: 0.239 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3APB Resolution: 1.92→34.01 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.919 / SU B: 3.499 / SU ML: 0.103 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.142 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.066 Å2
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Refinement step | Cycle: LAST / Resolution: 1.92→34.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.92→1.97 Å / Total num. of bins used: 20
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